Zinc in PDB 3wi2: Crystal Structure of PDE10A in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of PDE10A in Complex with Inhibitor:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A in Complex with Inhibitor, PDB code: 3wi2 was solved by Y.Amano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.115, 81.629, 158.084, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 32.9

The structure of Crystal Structure of PDE10A in Complex with Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE10A in Complex with Inhibitor (pdb code 3wi2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE10A in Complex with Inhibitor, PDB code: 3wi2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE10A in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:56.4 occ:1.00 OD2 A:ASP564 2.0 43.6 1.0 NE2 A:HIS529 2.1 32.9 1.0 OD1 A:ASP674 2.1 49.9 1.0 O A:HOH903 2.2 41.9 1.0 NE2 A:HIS563 2.2 38.4 1.0 CE1 A:HIS529 2.9 38.0 1.0 CD2 A:HIS563 3.1 39.3 1.0 O A:HOH901 3.1 37.8 1.0 CG A:ASP564 3.1 49.3 1.0 CG A:ASP674 3.1 47.3 1.0 CD2 A:HIS529 3.2 39.1 1.0 CE1 A:HIS563 3.3 37.4 1.0 OD2 A:ASP674 3.4 48.4 1.0 OD1 A:ASP564 3.7 50.9 1.0 O A:HOH905 3.7 45.0 1.0 MG A:MG802 3.7 48.0 1.0 ND1 A:HIS529 4.1 41.6 1.0 CG A:HIS529 4.2 37.4 1.0 CD2 A:HIS525 4.2 56.3 1.0 CG A:HIS563 4.3 44.4 1.0 CB A:ASP564 4.3 46.3 1.0 ND1 A:HIS563 4.3 44.2 1.0 CB A:ASP674 4.5 40.5 1.0 NE2 A:HIS525 4.6 54.5 1.0 CG2 A:VAL533 4.7 34.4 1.0 O A:HOH904 4.9 51.2 1.0 CA A:ASP674 4.9 38.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE10A in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:35.4 occ:1.00 NE2 B:HIS563 1.9 32.3 1.0 NE2 B:HIS529 2.0 37.1 1.0 OD2 B:ASP564 2.4 14.4 1.0 OD1 B:ASP674 2.5 15.0 1.0 CE1 B:HIS563 2.6 34.8 1.0 CE1 B:HIS529 3.0 43.8 1.0 CD2 B:HIS529 3.0 40.5 1.0 OD2 B:ASP674 3.0 17.4 1.0 CG B:ASP674 3.0 18.7 1.0 CD2 B:HIS563 3.1 39.5 1.0 CG B:ASP564 3.1 22.4 1.0 OD1 B:ASP564 3.2 22.1 1.0 ND1 B:HIS563 3.8 37.2 1.0 MG B:MG802 3.9 35.8 1.0 O B:HOH908 4.0 25.4 1.0 CG B:HIS563 4.0 32.8 1.0 ND1 B:HIS529 4.1 39.9 1.0 O B:HOH907 4.1 37.1 1.0 CG B:HIS529 4.1 38.5 1.0 CD2 B:HIS525 4.2 40.4 1.0 CB B:ASP674 4.6 28.6 1.0 CB B:ASP564 4.6 25.5 1.0 NE2 B:HIS525 4.6 42.6 1.0 CG2 B:VAL533 4.8 29.5 1.0 O B:ASP674 4.9 34.0 1.0

W.Hamaguchi, N.Masuda, M.Isomura, S.Miyamoto, S.Kikuchi, Y.Amano, K.Honbou, T.Mihara, T.Watanabe. Design and Synthesis of Novel Benzimidazole Derivatives As Phosphodiesterase 10A Inhibitors with Reduced CYP1A2 Inhibition. Bioorg.Med.Chem. 2013.
ISSN: ESSN 1464-3391
PubMed: 24238902
DOI: 10.1016/J.BMC.2013.10.035